Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008259.1 Corchorus capsularis cultivar CVL-1 contig08280, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 48187
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:798 original size:17 final size:18
Alignment explanation
Indices: 764--801 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
754 CCAAACCCAG
764 TGAGGAACAACATTAATGTT
1 TGAGGAACAAC--TAATGTT
784 TGAGGAACAAC-AATGTT
1 TGAGGAACAACTAATGTT
801 T
1 T
802 CATGTGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
20 11 0.61
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (18 bp):
TGAGGAACAACTAATGTT
Found at i:3122 original size:31 final size:31
Alignment explanation
Indices: 3041--3128 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
3031 TCCTTTTGTG
* *
3041 CACGTGACATGCCACGTGCCATTTTTTGAAA
1 CACGTGACATGCCACGTGTCACTTTTTGAAA
* * **
3072 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGACATGCCACGTGTCACTTTTTGAAA
* *
3103 CACGTGACATGACATGTGTCACTTTT
1 CACGTGACATGCCACGTGTCACTTTT
3129 AGTGCATGTG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (31 bp):
CACGTGACATGCCACGTGTCACTTTTTGAAA
Found at i:5822 original size:26 final size:26
Alignment explanation
Indices: 5786--5836 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
5776 GGGACTATAG
5786 AAATTGAATTTTTGTAAATAAAATAA
1 AAATTGAATTTTTGTAAATAAAATAA
5812 AAATTGAATTTTTGTAAATAAAATA
1 AAATTGAATTTTTGTAAATAAAATA
5837 TTTCAAGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (26 bp):
AAATTGAATTTTTGTAAATAAAATAA
Found at i:8079 original size:2 final size:2
Alignment explanation
Indices: 8019--8069 Score: 93
Period size: 2 Copynumber: 25.0 Consensus size: 2
8009 TTATCTTAGA
8019 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
8061 TC TC GTC TC
1 TC TC -TC TC
8070 CATCCTCTCT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 46 0.96
3 2 0.04
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
TC
Found at i:9664 original size:4 final size:4
Alignment explanation
Indices: 9657--9731 Score: 150
Period size: 4 Copynumber: 18.8 Consensus size: 4
9647 TATATATATA
9657 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9705 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
9732 CTGTTTATAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 71 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:9926 original size:15 final size:16
Alignment explanation
Indices: 9908--9940 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
9898 TATTAAATAA
9908 ATAATAATTATT-TTT
1 ATAATAATTATTATTT
9923 ATAATAATTATTATTT
1 ATAATAATTATTATTT
9939 AT
1 AT
9941 CCCATATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAATAATTATTATTT
Found at i:12712 original size:2 final size:2
Alignment explanation
Indices: 12705--12747 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
12695 GTCCACAACT
*
12705 TA TA TA TA CTC TA TA TA TA -A TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12746 TA
1 TA
12748 AACTAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 33 0.92
3 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12721 original size:11 final size:10
Alignment explanation
Indices: 12705--12747 Score: 54
Period size: 9 Copynumber: 4.4 Consensus size: 10
12695 GTCCACAACT
*
12705 TATATATACTC
1 TATATATA-TA
12716 TATATATA-A
1 TATATATATA
12725 TATATATATA
1 TATATATATA
12735 TATATATAT-
1 TATATATATA
12744 TATA
1 TATA
12748 AACTAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 12 0.40
10 10 0.33
11 8 0.27
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (10 bp):
TATATATATA
Found at i:29972 original size:22 final size:23
Alignment explanation
Indices: 29925--29972 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
29915 TAAATTGTCA
* *
29925 CAACTCAAATCATCTAAAAAATG
1 CAACTCAAACCATCTAAAAAACG
*
29948 CAACTCACACCATCT-AAAAACG
1 CAACTCAAACCATCTAAAAAACG
29970 CAA
1 CAA
29973 GAGATTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.50, C:0.29, G:0.04, T:0.17
Consensus pattern (23 bp):
CAACTCAAACCATCTAAAAAACG
Found at i:44727 original size:12 final size:13
Alignment explanation
Indices: 44710--44741 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
44700 CATGAAGCAA
44710 AAAAAAG-AAAAG
1 AAAAAAGAAAAAG
44722 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
44735 AAAAAAG
1 AAAAAAG
44742 GAAGAGGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:44727 original size:13 final size:14
Alignment explanation
Indices: 44709--44740 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
44699 CCATGAAGCA
44709 AAAAAAAG-AAAAG
1 AAAAAAAGAAAAAG
44722 -AAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
44735 AAAAAA
1 AAAAAA
44741 GGAAGAGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 5 0.29
14 5 0.29
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:45296 original size:2 final size:2
Alignment explanation
Indices: 45289--45325 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
45279 CTTAATACTT
45289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45326 GTGTTAAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45422 original size:23 final size:23
Alignment explanation
Indices: 45396--45443 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
45386 CAAGATGCTT
** *
45396 GACAATGACCATGCAAGTAGCTA
1 GACAATGACCAAACAAGTAGATA
45419 GACAATGACCAAACAAGTAGATA
1 GACAATGACCAAACAAGTAGATA
45442 GA
1 GA
45444 ACAACCATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.15
Consensus pattern (23 bp):
GACAATGACCAAACAAGTAGATA
Found at i:45710 original size:4 final size:4
Alignment explanation
Indices: 45701--45739 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
45691 GTAAACTTGT
*
45701 ATAC ATAC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
45740 GGTATTACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:47584 original size:12 final size:12
Alignment explanation
Indices: 47561--47592 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
47551 ATATATGTGA
47561 TATTTA-ATTTT
1 TATTTATATTTT
47572 TATTTATATTTT
1 TATTTATATTTT
47584 TATTTATAT
1 TATTTATAT
47593 CATTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTATATTTT
Found at i:47754 original size:13 final size:13
Alignment explanation
Indices: 47736--47760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47726 TTCAATATTG
47736 TAAATATTATTTA
1 TAAATATTATTTA
47749 TAAATATTATTT
1 TAAATATTATTT
47761 GGAGTTCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Done.